Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Open accessAbstract
Elimination of the data processing bottleneck in high-throughput sequencing will require both improved accuracy of data processing software and reliable measures of that accuracy. We have developed and implemented in our base-calling program phred the ability to estimate a probability of error for each base-call, as a function of certain parameters computed from the trace data. These error probabilities are shown here to be valid (correspond to actual error rates) and to have high power to discriminate correct base-calls from incorrect ones, for read data collected under several different chemistries and electrophoretic conditions. They play a critical role in our assembly program phrap and our finishing program consed.
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The inferred sequence accuracy in the muskox assembly coding regions is not less than 99.99910%, corresponding to a Phred score of not less than 50.4839.
“yields an inferred sequence accuracy in the assembly of not less than 99.99910%, corresponding to a Phred score54 of no less than 50.4839 in these coding regions.”
From Chromosomal-level reference genome assembly of muskox (Ovibos moschatus) from Banks Island in the Canadian Arctic, a resource for conservation genomics (2024) · cites this paper as [54]
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- Authors
- Ewing, B., & Green, P.
- Affiliations
- University of Washington (US)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 1998-03-01
- Volume
- 8
- Issue
- 3
- Pages
- 186-194
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- OpenAlex
- W2119923823
- Cited by
- 5,439
- References
- 8
- Citations by year
- 2026: 56 · 2025: 88 · 2024: 84 · 2023: 86 · 2022: 115 · 2021: 157 · 2020: 141 · 2019: 128 · 2018: 132 · 2017: 176 · 2016: 190 · 2015: 215 · 2014: 275 · 2013: 301 · 2012: 289
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Human Genome Research Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Keywords
- base calling, error probability estimation, next-generation sequencing, sequencing accuracy, genome assembly
- MeSH terms
- Base Sequence, Chimera, Cloning, Molecular, Data Interpretation, Statistical, Genetic Vectors, Humans, Probability, Quality Control, Software, Reproducibility of Results, Discriminant Analysis, Human Genome Project, Sequence Analysis, DNA
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